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A long-term annual crop study in Five Points, California, shows that the combined use of no-tillage, surface residue retention, and cover crops improves soil health compared to conventional practices common to the region. Several chemical, biological, and physical soil health indicators were improved when these practices were combined. Our data suggest that farmers stand to gain multiple synergistic benefits from the integrated use of these practices by increasing soil structural stability, water infiltration and storage, and agroecosystem biodiversity, and improving the efficiencies of the carbon, nitrogen, and water cycles of their production systems.

The introduction of novel perennial grains into annual row crop rotations is proposed to increase soil ecosystem services and enhance plant-soil-microbial linkages because perennials provide deeper root systems and more continuous ground cover than annuals. While soil microbial communities underpin many ecosystem services, we know little about how soil microbial composition and diversity, and soil carbon storage, differ between soils of annual vs. perennial grain crops. We measured soil fungi: bacteria (F/B) ratios and soil carbon within the novel perennial intermediate wheatgrass (IWG; trademarked Kernza®) and tilled annual wheat and compared soil microbial diversity and community composition within their rhizosphere, shallow bulk soil (0–15 cm) and total bulk soil (0–90 cm). After three years, soil depth explained 30–40% and 12–22% of the variance in bacterial and fungal community composition, respectively, while crop type explained 10% and 9–16% of the variance, respectively. Fungal communities were most impacted by crop type in the rhizosphere and shallow bulk soil and less sensitive to differences in soil depth. In contrast, crop type had a smaller effect on bacterial communities which were more influenced by soil depth. IWG trended higher in soil carbon mass at 0–30 cm (p = 0.22) and had a higher (F/B) ratio than tilled annual wheat at depths below 15 cm, but tilled annual wheat had higher soil carbon concentration (p = 0.12) and soil carbon mass (p = 0.09) at the 60–90 cm soil depth. Our results indicate that fungi were more responsive than bacterial communities to crop type and that IWG has a higher fungal biomass and different fungal community composition than annual wheat at depth. However, despite these distinct differences in fungal communities in IWG compared to annual wheat, the differences did not translate into greater soil carbon mass in IWG at depth.

Adding manure to croplands restores carbon and nutrients in depleted soils, while addressing a waste disposal need. This practice depends on the abundance and activity of microbial communities to break down manure inputs, which provide carbon for microbial growth and release nutrients for plant and microbial uptake. In a 2-year field study, we measured changes to soil physicochemical properties and microbial community composition in a conventional rotation of summer sileage corn and winter wheat. Three ratios of manure to mineral N fertilizer were used: all manure (100% of plant N from manure), mixed (50% plant N from by manure and 50% from mineral fertilizer), and all mineral (100% plant N from mineral fertilizer). Yields of corn and wheat were similar across treatments. Soil microbial community dissimilarity increased with higher ratios of application, suggesting a dose-dependent relationship between manure application and microbial community composition. Both microbial biomass and dissolved organic carbon showed the greatest response immediately following manure application, then decreased until the next application. The Shannon index increased shortly after manure application, with the largest increase observed in soils receiving manure input. Many of the taxa that increased in relative abundance following manure application were specifically taxa known to be present in manure and not common or present in soil before manure application. Microbial community changes following manure application were transitory, indicating that without continual inputs of resources, these alterations are not maintained. This was in contrast to microbial biomass which slowly increased in size over the 2-year study period. Better understanding of how manure interacts with microbial communities will help in developing better nutrient management practices and help reduce our reliance on mineral fertilizers.

Soil organic amendments in agricultural production can benefit crop production and a wide range of soil properties, including soil aggregation. Soil aggregate formation is largely driven by microbial activities, and can in-turn influence microbial communities by generating distinct microbial habitats, as well as associated impacts on water and nutrient dynamics. We investigated the long-term effects of two fertilizer management strategies (poultry manure compost vs. mineral fertilizer) and biochar amendment (0 vs. 10 t ha−1 walnut shell biochar, 900 °C pyrolysis temperature, by-product of gasification) on soil aggregation, soil organic C, and microbial community dynamics in water-stable aggregate fractions in corn-tomato rotations. Using wet-sieving, soils (0–15 cm) were divided into four size fractions: large macroaggregates (2000–8000 μm), small macroaggregates (250–2000 μm), microaggregates (53–250 μm) and silt and clay (

Copper (Cu) products, including copper oxide nanoparticles (nCuO), are critically important agricultural fungicides and algaecides. Foliar application onto crops and subsequent aerosol drift of these Cu products, especially nCuO, on to soil may alter nutrient cycling and microbial communities in both managed and unmanaged environments. We measured the influence of land use on soil microbial biomass and respiration in response to the addition of nCuO to an alluvial soil. Different land uses included grassland, forest and both organic and conventional managed row crops. Soil samples were amended with 1000 mg Cu per kg soil as CuCl2, 16 nm CuO (16nCuO), 42 nm CuO (42nCuO), and larger than nanoparticle sized bulk CuO (bCuO). Copper availability immediately increased in all soils following Cu addition in the order of CuCl2 > 16nCuO > 42nCuO > bCuO. After 70 days Cu availability was diminished across land uses and lowest in soils treated with bCuO. Using X-ray absorption near edge structure (XANES) spectroscopy, we determined that the relatively high availability of Cu after treatment with nanoparticle sized CuO was due to the dissolution of CuO particles and subsequent adsorption by soil materials. Respiration, an indicator of microbial activity, was suppressed by Cu additions, especially CuCl2. Copper effects on soil microbial biomass were sensitive to land use. In agricultural soils, microbial biomass was unaltered by Cu form, regardless of concentration, whereas in unmanaged soils, it decreased following exposure to CuCl2 and 42nCuO. Our results suggest that land use history has little impact on Cu chemical fate in soils, but strongly modulates microbial response to Cu exposure. These results are especially important for organic agricultural systems where copper fungicides are widely used but may suppress microbial mineralization of nutrients from soil organic matter.

Soil and soil biodiversity play critical roles in Nature's Contributions to People (NCP) # 10, defined as Nature's ability to regulate direct detrimental effects on humans, and on human-important plants and animals, through the control or regulation of particular organisms considered to be harmful. We provide an overview of pathogens in soil, focusing on human and crop pathogens, and discuss general strategies, and examples, of how soils' extraordinarily diverse microbial communities regulate soil-borne pathogens. We review the ecological principles underpinning the regulation of soil pathogens, as well as relationships between pathogen suppression and soil health. Mechanisms and specific examples are presented of how soil and soil biota are involved in regulating pathogens of humans and plants. We evaluate how specific agricultural management practices can either promote or interfere with soil's ability to regulate pathogens. Finally, we conclude with how integrating soil, plant, animal and human health through a 'One Health' framework could lead to more integrated, efficient and multifunctional strategies for regulating detrimental organisms and processes. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People'.

This special issue provides an assessment of the contribution of soils to Nature's Contributions to People (NCP). Here, we combine this assessment and previously published relationships between NCP and delivery on the UN Sustainable Development Goals (SDGs) to infer contributions of soils to the SDGs. We show that in addition to contributing positively to the delivery of all NCP, soils also have a role in underpinning all SDGs. While highlighting the great potential of soils to contribute to sustainable development, it is recognized that poorly managed, degraded or polluted soils may contribute negatively to both NCP and SDGs. The positive contribution, however, cannot be taken for granted, and soils must be managed carefully to keep them healthy and capable of playing this vital role. A priority for soil management must include: (i) for healthy soils in natural ecosystems, protect them from conversion and degradation; (ii) for managed soils, manage in a way to protect and enhance soil biodiversity, health and sustainability and to prevent degradation; and (iii) for degraded soils, restore to full soil health. We have enough knowledge now to move forward with the implementation of best management practices to maintain and improve soil health. This analysis shows that this is not just desirable, it is essential if we are to meet the SDG targets by 2030 and achieve sustainable development more broadly in the decades to come. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People'.

Root exploitation of soil heterogeneity and microbially mediated rhizosphere nutrient transformations play critical roles in plant resource uptake. However, how these processes change under water-saving irrigation technologies remains unclear, especially for organic systems where crops rely on soil ecological processes for plant nutrition and productivity. We conducted a field experiment and examined how water-saving subsurface drip irrigation (SDI) and concentrated organic fertilizer application altered root traits and rhizosphere processes compared to traditional furrow irrigation (FI) in an organic tomato system. We measured root distribution and morphology, the activities of C-, N-, and P-cycling enzymes in the rhizosphere, the abundance of rhizosphere microbial N-cycling genes, and root mycorrhizal colonization rate under two irrigation strategies. Tomato plants produced shorter and finer root systems with higher densities of roots around the drip line, lower activities of soil C-degrading enzymes, and shifts in the abundance of microbial N-cycling genes and mycorrhizal colonization rates in the rhizosphere of SDI plants compared to FI. SDI led to 66.4% higher irrigation water productivity than FI, but it also led to excessive vegetative growth and 28.3% lower tomato yield than FI. Our results suggest that roots and root-microbe interactions have a high potential for coordinated adaptation to water and nutrient spatial patterns to facilitate resource uptake under SDI. However, mismatches between plant needs and resource availability remain, highlighting the importance of assessing temporal dynamics of root-soil-microbe interactions to maximize their resource-mining potential for innovative irrigation systems.

Increasing soil organic carbon (SOC) via organic inputs is a key strategy for increasing long-term soil C storage and improving the climate change mitigation and adaptation potential of agricultural systems. A long-term trial in California's Mediterranean climate revealed impacts of management on SOC in maize-tomato and wheat-fallow cropping systems. SOC was measured at the initiation of the experiment and at year 19, at five depth increments down to 2 m, taking into account changes in bulk density. Across the entire 2 m profile, SOC in the wheat-fallow systems did not change with the addition of N fertilizer, winter cover crops (WCC), or irrigation alone and decreased by 5.6% with no inputs. There was some evidence of soil C gains at depth with both N fertilizer and irrigation, though high variation precluded detection of significant changes. In maize-tomato rotations, SOC increased by 12.6% (21.8 Mg C/ha) with both WCC and composted poultry manure inputs, across the 2 m profile. The addition of WCC to a conventionally managed system increased SOC stocks by 3.5% (1.44 Mg C/ha) in the 0-30 cm layer, but decreased by 10.8% (14.86 Mg C/ha) in the 30-200 cm layer, resulting in overall losses of 13.4 Mg C/ha. If we only measured soil C in the top 30 cm, we would have assumed an increase in total soil C increased with WCC alone, whereas in reality significant losses in SOC occurred when considering the 2 m soil profile. Ignoring the subsoil carbon dynamics in deeper layers of soil fails to recognize potential opportunities for soil C sequestration, and may lead to false conclusions about the impact of management practices on C sequestration.

Adaptive management practices that maximize yields while improving yield resilience are required in the face of resource variability and climate change. Ecological intensification such as organic farming and cover cropping are lauded in some studies for fostering yield resilience, but subject to criticism in others for their low productivity. We implemented a quantitative framework to assess yield resilience, emphasizing four aspects of yield dynamics: yield, yield stability, yield resistance (i.e., the ability of systems to avoid crop failure under stressful growing conditions), and maximum yield potential. We compared the resilience of maize-tomato rotation systems after 24 years of irrigated organic, cover cropped, and conventional management in a Mediterranean climate, and identified crop-specific resilience responses of tomato and maize to three management systems. Organic management maintained tomato yields comparable to those under conventional management, while increasing yield stability and resistance. However, organic and cover cropped system resulted in 36.1% and 35.8% lower maize yields and reduced yield stability and resistance than the conventional system. Our analyses suggest that investments in ecological intensification approaches could potentially contribute to long-term yield resilience, however, these approaches need to be tailored for individual crops and systems to maximize their benefits, rather than employing one-size-fits-all approaches.

Nitrogen is a critical component of the economy, food security, and planetary health. Many of the world's sustainability targets hinge on global nitrogen solutions, which, in turn, contribute lasting benefits for: (i) world hunger; (ii) soil, air and water quality; (iii) climate change mitigation; and (iv) biodiversity conservation. Balancing the projected rise in agricultural nitrogen demands while achieving these 21st century ideals will require policies to coordinate solutions among technologies, consumer choice, and socioeconomic transformation.

The ability of soil to retain water under drought and other extreme hydrological events is critical to the sustainability of food production systems and preserving soil ecosystem services. We investigated the impact of biochar on water retention properties in California agricultural soils in a series of column, lab incubation, and field studies. Results from studies based on similar variables (soil, biochar) were used to demonstrate the impact of biochar on soil-water relations at different scales. The influences of biochar type (softwood, 600–700 °C, low surface area; walnut shell, 900 °C, high surface area), application rate (0, 0.5, 1% wt.), and particle diameter (0–0.25, 0.25–0.5, 0.5–1, 1–2 mm) were investigated. Only the higher surface area biochar increased the field capacity of a sandy soil. Neither biochar, altered the field capacity of the higher clay content soil. The walnut shell biochar with 1–2 mm particle diameter was more effective at increasing field capacity in sandy soils compare to smaller biochar size fractions. Neither biochar affected the wilting point in either soil. Neutron imaging was used to explore potential mechanisms involved in water retention by observing the spatial and temporal distribution of water in and surrounding biochar particles (~ 2 mm diameter). After wetting, water retained in the internal pores of biochar was continuously released to surrounding space (~ 2.2 mm sphere) during a 7-day air drying at room temperature, suggesting that soil water retention is improved via the biochar's intraparticle structure. In the field trial, (6 yr., corn-tomato rotation), neither walnut shell biochar amendment (10 t/ ha, equivalent to 0.5% wt. in lab scale experiments) nor agricultural management practices (organic, conventional) altered the water retention capacity of a silty clay loam soil. These data suggest that biochars with a high pore volume can temporarily increase the field capacity and plant available water in a coarse-textured soil, until biochar internal pores are filled by clay and soil organic matter. Our results suggest that biochar can have a limited impact on soil water retention when biochar pore volume is low, or soil texture is fine. High dosage (≥10 t/ha) of high pore volume biochar with bulky particle size (≥1 mm) can improve water retention of coarse-textured soil with limited capacity of water storage and may improve soil's resilience during hydrological extremes.

Fungi are important members of soil microbial communities in row-crop and grassland soils, provide essential ecosystem services such as nutrient cycling, organic matter decomposition, and soil structure, but fungi are also more sensitive to physical disturbance than other microorganisms. Adoption of conservation management practices such as no-till and cover cropping shape the structure and function of soil fungal communities. No-till eliminates or greatly reduces the physical disturbance that re-distributes organisms and nutrients in the soil profile and disrupts fungal hyphal networks, while cover crops provide additional types and greater abundance of organic carbon sources. In a long-term, row crop field experiment in California's Central Valley we hypothesized that a more diverse and plant symbiont-enriched fungal soil community would develop in soil managed with reduced tillage practices and/or cover crops compared to standard tillage and no cover crops. We measured the interacting effects of tillage and cover cropping on fungal communities based on fungal ITS sequence assigned to ecological guilds. Functional groups within fungal communities were most sensitive to long-term tillage practices, with 45% of guild-assigned taxa responding to tillage, and a higher proportion of symbiotroph taxa under no-till. In contrast, diversity measures reflected greater sensitivity to cover crops, with higher phylogenetic diversity observed in soils managed with cover crops, though only 10% of guild-assigned taxa responded to cover crops. The relative abundance of pathotrophs did not vary across the management treatments. Cover cropping increased species diversity, while no-till shifted the symbiotroph:saprotroph ratio to favor symbiotrophs. These management-induced shifts in fungal community composition could lead to greater ecosystem resilience and provide greater access of crops to limiting resources.

Nitrogen is a critical component of the economy, food security, and planetary health. Many of the world's sustainability targets hinge on global nitrogen solutions, which, in turn, contribute lasting benefits for: (i) world hunger; (ii) soil, air and water quality; (iii) climate change mitigation; and (iv) biodiversity conservation. Balancing the projected rise in agricultural nitrogen demands while achieving these 21st century ideals will require policies to coordinate solutions among technologies, consumer choice, and socioeconomic transformation.

The Century Experiment at the Russell Ranch Sustainable Agriculture Facility at the University of California, Davis provides long-term agroecological data from row crop systems in California's Central Valley starting in 1993. The Century Experiment was initially designed to study the effects of a gradient of water and nitrogen availability on soil properties and crop performance in ten different cropping systems to measure tradeoffs and synergies between agricultural productivity and sustainability. Currently systems include 11 different cropping systems-consisting of four different crops and a cover crop mixture-and one native grass system. This paper describes the long-term core data from the Century Experiment from 1993-2014, including crop yields and biomass, crop elemental contents, aerial-photo-based Normalized Difference Vegetation Index data, soil properties, weather, chemical constituents in irrigation water, winter weed populations, and operational data including fertilizer and pesticide application amounts and dates, planting dates, planting quantity and crop variety, and harvest dates. This data set represents the only known long-term set of data characterizing food production and sustainability in irrigated and rainfed Mediterranean annual cropping systems. There are no copyright restrictions associated with the use of this dataset.

Reducing tillage and growing cover crops, widely recommended practices for boosting soil health, have major impacts on soil communities. Surprisingly little is known about their impacts on soil microbial functional diversity, and especially so in irrigated Mediterranean ecosystems. In long-term experimental plots at the West Side Research and Extension Center in California's Central Valley, we characterized soil microbial communities in the presence or absence of physical disturbance due to tillage, in the presence or absence of cover crops, and at three depths: 0-5, 5-15 and 15-30 cm. This characterization included qPCR for bacterial and archaeal abundances, DNA sequencing of the 16S rRNA gene, and phylogenetic estimation of two ecologically important microbial traits (rRNA gene copy number and genome size). Total (bacterial + archaeal) diversity was higher in no-till than standard till; diversity increased with depth in no-till but decreased with depth in standard till. Total bacterial numbers were higher in cover cropped plots at all depths, while no-till treatments showed higher numbers in 0-5 cm but lower numbers at lower depths compared to standard tillage. Trait estimates suggested that different farming practices and depths favored distinctly different microbial life strategies. Tillage in the absence of cover crops shifted microbial communities towards fast growing competitors, while no-till shifted them toward slow growing stress tolerators. Across all treatment combinations, increasing depth resulted in a shift towards stress tolerators. Cover crops shifted the communities towards ruderals-organisms with wider metabolic capacities and moderate rates of growth. Overall, our results are consistent with decreasing nutrient availability with soil depth and under no-till treatments, bursts of nutrient availability and niche homogenization under standard tillage, and increases in C supply and variety provided by cover crops. Understanding how agricultural practices shift microbial abundance, diversity and life strategies, such as presented here, can assist with designing farming systems that can support high yields, while enhancing C sequestration and increasing resilience to climate change.

Shallow, small-rate releases of ethanol-blended fuels from underground storage tanks (USTs) may be quite common and result in subsurface CH4 generation. However, vadose zone transport of CH4 generated from these fuel releases is poorly understood, despite the potential to promote vapor intrusion or create explosion hazards. In this study, we simulated shallow CH4 generation with a controlled subsurface CH4 release from July 2014 to February 2015 to characterize subsurface CH4 migration and surface emissions and to determine environmental controls on CH4 fate and transport. July 2014 through November 2014 was an extended period of drought followed by precipitation during December 2014. Throughout the experiment, under varied CH4 injection rates, CH4 formed a radially symmetrical plume around the injection point. Surface efflux during the drought period of the experiment was relatively high and stable, with approximately 10 to 11 and 34 to 52% of injected CH4 reaching the ground surface during the low-and high-rate injections, respectively. Following the period of precipitation and increased soil moisture, efflux dropped and stabilized at approximately 1% of injected CH4, even as soil moisture began to decrease again. Tracer and inhibitor experiments and estimates of soil diffusivity suggest that microbial CH4 oxidation was responsible for the observed drop in efflux. The decrease in efflux only after soil moisture increased suggests a strong environmental control over the transport and oxidation of vadose zone CH4.

Agriculture in California contributes 8% of the state's greenhouse gas (GHG) emissions. To inform the state's policy and program strategy to meet climate targets, we review recent research on practices that can reduce emissions, sequester carbon and provide other co-benefits to producers and the environment across agriculture and rangeland systems. Importantly, the research reviewed here was conducted in California and addresses practices in our specific agricultural, socioeconomic and biophysical environment. Farmland conversion and the dairy and intensive livestock sector are the largest contributors to GHG emissions and offer the greatest opportunities for avoided emissions. We also identify a range of other opportunities including soil and nutrient management, integrated and diversified farming systems, rangeland management, and biomass-based energy generation. Additional research to replicate and quantify the emissions reduction or carbon sequestration potential of these practices will strengthen the evidence base for California climate policy.

California's Mediterranean agro-ecosystems are a major source of U.S. fruits and vegetables, and vulnerable to future extremes of precipitation and temperature brought on by climate change, including increased drought and flooding, and more intense and longer heat waves. To develop resilience to these threats, strategies are necessary for climate-smart management of soil and water. Long-term, large-scale, replicated ecological experiments provide unique testbeds for studying such questions. At the UC Davis Russell Ranch Sustainable Agriculture Facility (RRSAF), the 100-year Century Experiment, initiated in 1992, is investigating the effects of multiple farming practices in a farm-scale replicated study of 10 row crop cropping systems. It includes different fertility management systems: organic, conventional and hybrid (conventional plus winter cover crop) systems; different crops: wheat, tomatoes, corn, alfalfa, cover crops and grasslands; and different irrigation systems: rainfed, flood irrigated and drip irrigated. We briefly describe and report on a selection of long-term experiments conducted at RRSAF investigating soil management and irrigation practices, which are an important focus for developing climate-smart strategies in Mediterranean systems. For example, long-term monitoring of soil carbon content revealed that most crop systems have experienced a small increase in soil carbon since 1993, and increases in organically managed plots were substantially higher. As RRSAF continues to build upon this rich dataset from one of a very few long-term row crop experiments in Mediterranean ecosystems, it provides a testbed for identifying climate-smart solutions for these agronomically important ecosystems.

Methyl-tert-butyl ether (MTBE) and its degradation by-product, tert-butyl alcohol (TBA), are widespread contaminants detected frequently in groundwater in California. Since MTBE was used as a fuel oxygenate for almost two decades, leaking underground fuel storage tanks are an important source of contamination. Gasoline components such as BTEX (benzene, toluene, ethylbenzene and xylenes) are often present in mixtures with MTBE and TBA. Investigations of interactions between BTEX and MTBE degradation have not yielded consistent trends, and the molecular mechanisms of BTEX compounds' impact on MTBE degradation are not well understood. We investigated trends in transcription of biodegradation genes in the MTBE-degrading bacterium, Methylibium petroleiphilum PM1 upon exposure to MTBE, TBA, ethylbenzene and benzene as individual compounds or in mixtures. We designed real-time quantitative PCR assays to target functional genes of strain PM1 and provide evidence for induction of genes mdpA (MTBE monooxygenase), mdpJ (TBA hydroxylase) and bmoA (benzene monooxygenase) in response to MTBE, TBA and benzene, respectively. Delayed induction of mdpA and mdpJ transcription occurred with mixtures of benzene and MTBE or TBA, respectively. bmoA transcription was similar in the presence of MTBE or TBA with benzene as in their absence. Our results also indicate that ethylbenzene, previously proposed as an inhibitor of MTBE degradation in some bacteria, inhibits transcription of mdpA, mdpJ and bmoAgenes in strain PM1.

ObjectivesFood insecurity and HIV/AIDS outcomes are inextricably linked in sub-Saharan Africa. We report on health and nutritional outcomes of a multisectoral agricultural intervention trial among HIV-infected adults in rural Kenya.DesignThis is a pilot cluster randomized controlled trial.MethodsThe intervention included a human-powered water pump, a microfinance loan to purchase farm commodities, and education in sustainable farming practices and financial management. Two health facilities in Nyanza Region, Kenya were randomly assigned as intervention or control. HIV-infected adults 18 to 49 years' old who were on antiretroviral therapy and had access to surface water and land were enrolled beginning in April 2012 and followed quarterly for 1 year. Data were collected on nutritional parameters, CD4 T-lymphocyte counts, and HIV RNA. Differences in fixed-effects regression models were used to test whether patterns in health outcomes differed over time from baseline between the intervention and control arms.ResultsWe enrolled 72 and 68 participants in the intervention and control groups, respectively. At 12 months follow-up, we found a statistically significant increase in CD4 cell counts (165 cells/μl, P

Biochar is increasingly been used as a soil amendment to improve water-holding capacity, reduce nutrient leaching, increase soil pH, and also as a means to reduce contamination through sorption of heavy metals or organic pollutants. The sorption behavior of three phenylurea herbicides (monuron, diuron and linuron) on five biochars (Enhanced Biochar, Hog Waste, Turkey Litter, Walnut Shell and Wood Feedstock) and an agricultural soil (Yolo silt loam) was investigated using a batch equilibration method. Sorption isotherms of herbicides to biochars were well described by the Freundlich model (R(2) = 0.93-0.97). The adsorption KF values ranged from 6.94 to 1306.95 mg kg(-1) and indicated the sorption of herbicides in the biochars and Yolo soil was in the sequence of linuron > diuron > monuron and walnut shell biochar > wood feedstock biochar > turkey litter biochar > enhanced biochar > hog waste biochar > Yolo soil. These data show that sorption of herbicides to biochar can have both positive (reduced off-site transport) and negative (reduced herbicide efficacy) implications and specific biochar properties, such as H/C ratio and surface area, should be considered together with soil type, agriculture chemical and climate condition in biochar application to agricultural soil to optimize the system for both agricultural and environmental benefits.

Among the few bacteria known to utilize methyl tert-butyl ether (MTBE) as a sole carbon source, Methylibium petroleiphilum PM1 is a well-characterized organism with a sequenced genome; however, knowledge of the genetic regulation of its MTBE degradation pathway is limited. We investigated the role of a putative transcriptional activator gene, mdpC, in the induction of MTBE-degradation genes mdpA (encoding MTBE monooxygenase) and mdpJ (encoding tert-butyl alcohol hydroxylase) of strain PM1 in a gene-knockout mutant mdpC(-). We also utilized quantitative reverse transcriptase PCR assays targeting genes mdpA, mdpJ and mdpC to determine the effects of the mutation on transcription of these genes. Our results indicate that gene mdpC is involved in the induction of both mdpA and mdpJ in response to MTBE and tert-butyl alcohol (TBA) exposure in PM1. An additional independent mechanism may be involved in the induction of mdpJ in the presence of TBA.

Triclosan (TCS) is a widely used antimicrobial agent found at high concentrations in biosolids produced during municipal wastewater treatment. The effect of adding TCS, in the presence or absence of biosolids, on the composition of an agricultural soil microbial community was measured using phospholipid fatty acid analysis (PLFA). Most changes observed in microbial community composition were attributable to the addition of biosolids or to the passage of time, with smaller changes due to TCS exposure, regardless of the presence of biosolids. TCS slightly reduced the relative abundance of Gram-positive and Gram-negative bacteria and fungi, with or without biosolids. Bacteria were more sensitive than eukaryotes, consistent with the mode of action of TCS, which selectively targets fatty acid synthesis and disrupts cell membranes of bacteria. TCS slightly increased biomarkers of microbial stress, but stress biomarkers were lower in all biosolid treated soils, presumably due to increased availability of nutrients mitigating potential TCS toxicity.

Although the anaerobic biodegradation of methyl tert-butyl ether (MTBE) and tert-butyl alcohol (TBA) has been documented in the laboratory and the field, knowledge of the microorganisms and mechanisms involved is still lacking. In this study, DNA-stable isotope probing (SIP) was used to identify microorganisms involved in anaerobic fuel oxygenate biodegradation in a sulfate-reducing MTBE and TBA plume. Microorganisms were collected in the field using Bio-Sep® beads amended with 13C5-MTBE, 13C1-MTBE (only methoxy carbon labeled), or13C4-TBA. 13C-DNA and 12C-DNA extracted from the Bio-Sep beads were cloned and 16S rRNA gene sequences were used to identify the indigenous microorganisms involved in degrading the methoxy group of MTBE and the tert-butyl group of MTBE and TBA. Results indicated that microorganisms were actively degrading 13C-labeled MTBE and TBA in situ and the 13C was incorporated into their DNA. Several sequences related to known MTBE- and TBA-degraders in the Burkholderiales and the Sphingomonadales orders were detected in all three13C clone libraries and were likely to be primary degraders at the site. Sequences related to sulfate-reducing bacteria and iron-reducers, such as Geobacter and Geothrix, were only detected in the clone libraries where MTBE and TBA were fully labeled with 13C, suggesting that they were involved in processing carbon from the tert-butyl group. Sequences similar to the Pseudomonas genus predominated in the clone library where only the methoxy carbon of MTBE was labeled with 13C. It is likely that members of this genus were secondary degraders cross-feeding on 13C-labeled metabolites such as acetate.

Conservative tracer experiments can provide information useful for characterizing various subsurface transport properties. This study examines the effectiveness of three different types of transport observations for sensitivity analysis and parameter estimation of a three-dimensional site-specific groundwater flow and transport model: conservative tracer breakthrough curves (BTCs), first temporal moments of BTCs (m1), and tracer cumulative mass discharge (Md) through control planes combined with hydraulic head observations (h). High-resolution data obtained from a 410-day controlled field experiment at Vandenberg Air Force Base, California (USA), have been used. In this experiment, bromide was injected to create two adjacent plumes monitored at six different transects (perpendicular to groundwater flow) with a total of 162 monitoring wells. A total of 133 different observations of transient hydraulic head, 1,158 of BTC concentration, 23 of first moment, and 36 of mass discharge were used for sensitivity analysis and parameter estimation of nine flow and transport parameters. The importance of each group of transport observations in estimating these parameters was evaluated using sensitivity analysis, and five out of nine parameters were calibrated against these data. Results showed the advantages of using temporal moment of conservative tracer BTCs and mass discharge as observations for inverse modeling.

In a field experiment at Vandenberg Air Force Base (VAFB) designed to mimic the impact of a small-volume release of E10 (10% ethanol and 90% conventional gasoline), two plumes were created by injecting extracted groundwater spiked with benzene, toluene, and o-xylene, abbreviated BToX (No-Ethanol Lane) and BToX plus ethanol (With-Ethanol Lane) for 283 days. We developed a reactive transport model to understand processes controlling the fate of ethanol and BToX. The model was calibrated to the extensive field dataset and accounted for concentrations of sulfate, iron, acetate, and methane along with iron-reducing bacteria, sulfate-reducing bacteria, fermentative bacteria, and methanogenic archaea. The benzene plume was about 4.5 times longer in the With-Ethanol Lane than in the No-Ethanol Lane. Matching this different behavior in the two lanes required inhibiting benzene degradation in the presence of ethanol. Inclusion of iron reduction with negligible growth of iron-reducers was required to reproduce the observed constant degradation rate of benzene. Modeling suggested that vertical dispersion and diffusion of sulfate from an adjacent aquitard were important sources of sulfate in the aquifer. Matching of methane data required incorporating initial fermentation of ethanol to acetate, methane loss by outgassing, and methane oxidation coupled to sulfate and iron reduction. Simulation of microbial growth using dual Monod kinetics, and including inhibition by more favorable electron acceptors, generally resulted in reasonable yields for microbial growth of 0.01-0.05.

Agricultural practices have proven to be unsuitable in many cases, causing considerable reductions in soil quality. Land management practices can provide solutions to this problem and contribute to get a sustainable agriculture model. The main objective of this work was to assess the effect of different agricultural management practices on soil microbial community structure (evaluated as abundance of phospholipid fatty acids, PLFA). Five different treatments were selected, based on the most common practices used by farmers in the study area (eastern Spain): residual herbicides, tillage, tillage with oats and oats straw mulching; these agricultural practices were evaluated against an abandoned land after farming and an adjacent long term wild forest coverage. The results showed a substantial level of differentiation in the microbial community structure, in terms of management practices, which was highly associated with soil organic matter content. Addition of oats straw led to a microbial community structure closer to wild forest coverage soil, associated with increases in organic carbon, microbial biomass and fungal abundances. The microbial community composition of the abandoned agricultural soil was characterised by increases in both fungal abundances and the metabolic quotient (soil respiration per unit of microbial biomass), suggesting an increase in the stability of organic carbon. The ratio of bacteria:fungi was higher in wild forest coverage and land abandoned systems, as well as in the soil treated with oat straw. The most intensively managed soils showed higher abundances of bacteria and actinobacteria. Thus, the application of organic matter, such as oats straw, appears to be a sustainable management practice that enhances organic carbon, microbial biomass and activity and fungal abundances, thereby changing the microbial community structure to one more similar to those observed in soils under wild forest coverage.

The climate of California is predicted to change significantly during the coming century. Whilea changing climate will impact the stateas a whole, some sectors may be impacted more than others. This is especially true of agriculture. Impacts may not only alter the types and locations of commodities produced, but also the factors influencing their production, such as resource availability and biotic and abiotic stresses. The nature and interrelatedness of these factors, and the response of agro-ecosystems, need to be explored to effectively mitigate and/or adapt to the effectsof climate change in a sustainable manner.To consider the challenges facing California agriculture in a changing climate, a symposium entitled “Climate Change: Challenges and Solutions for California Agricultural Landscapes” was held at University of California, Davis, by the John Muir Institute for the Environment, May 12-13 2005 (John Muir Institute 2005). Talks were presented by 29 speakers from West Coast Universities and state and federal agencies, to an audience of more than 100 participants from a range of organizations and stakeholder groups. The structure of the symposium promoted open discussion among participants from multiple disciplines. The presentations and conclusions of the symposium provide the basic structure and foundation upon which this report is written.An important outcome of the symposium was recognition not only of future impacts of climate change on California agricultural landscapes, but of the fact that actions taken now and in the near future will play critical roles in dealing with these changes. By taking a landscape perspective, the focus was not only on commodity-specific issues and agro-ecosystem changes, but also included a wider range of ecosystems, such as water availability and transport, and interactions with urban ecosystems. As such, there is a greater need than ever to train scientists with a broad and in-depth appreciation of the complex issues of climate change. To this end, we developed a graduate-level seminar class entitled Climate Change and the California Agricultural Landscape (ECL/SSC 290) UC Davis (July-Sept, 2005). Fourteen graduate students, from both the Ecology and the Soils and Biogeochemistry Graduate Groups, participated in the class. Student workgroups, mentored by UC Davis faculty and/or a representative from a government agency, integrated material from the symposium presentations and a review of the scientific literature to identify key impacts of climate change upon California agricultural landscapes.Adhering, for the most part, to the organizational structure of the symposium, this report consists of an integrated analysis of potential impacts of climate change upon California agriculture. It primarily focuses on identifying impacts, options for adaptation, and identification of areas where key data are currently lacking. California agriculture also has an important role to play in climate change mitigation, both in the short term and in the longer term. This report, also identifies areas and options where California agriculture may act as a net mitigator of climate change. Another outcome of this effort is a database of >500 references relevant to assessment of climate change in California agricultural landscapes

Widespread contamination of groundwater by methyl tertiary butyl ether (MTBE) has triggered the exploration of different technologies for in situ removal of the pollutant, including biostimulation of naturally occurring microbial communities or bioaugmentation with specific microbial strains known to biodegrade the oxygenate. After laboratory studies revealed that bacterial strain PM1 rapidly and completely biodegraded MTBE in groundwater sediments, the organism was tested in an in situ field study at Port Hueneme Naval Construction Battalion Center in Oxnard, California. Two pilot test plots (A and B) in groundwater located down-gradient from an MTBE source were intermittently sparged with pure oxygen. Plot B was also inoculated with strain PM1. MTBE concentrations up-gradient from plots A and B initially varied temporally from 1.5 to 6 mg MTBE/L. Six months after treatment began, MTBE concentrations in monitoring wells down-gradient from the injection bed decreased substantially in the shallow zone of the groundwater in plots A and B, thus even in the absence of the inoculated strain PM1. In the deeper zone, downstream MTBE concentrations also decreased in plot A and to a lesser extent in plot B. Difficulties in delivery of oxygen to the deeper zone of plot B, evidenced by low dissolved oxygen concentrations, were likely responsible for low rates of MTBE removal at that location. We measured the survival and movement of strain PM1 in groundwater samples using two methods for detection of DNA sequences specific to strain PM1: TaqMan quantitative polymerase chain reaction, and internal transcribed spacer region analysis. A naturally occurring bacterial strain with > 99% 16S rDNA sequence similarity to strain PM1 was detected in groundwater collected at various locations at Port Hueneme, including outside the plots where the organism was inoculated. Addition of oxygen to naturally occurring microbial populations was sufficient to stimulate MTBE removal at this site. In some cases, however, inoculation with an MTBE-degrading culture may be warranted.

Methyl bromide is highly effective in reducing soil pathogens. Although its use was to be phased out completely in the United States by Jan. 1, 2005, due to environmental concerns, a 1-year critical-use exemption will allow tree fruit growers to use the fumigant through the end of the year. To explore possible replacements for methyl bromide, we compared the effects of pre- and postplant treatments and amendments on soil microbial communities and tree vigor in a replanted peach orchard. Both soil sterilization treatments and organic carbon amendments changed the composition of microbial communities in the soil. High microbial biomass is generally considered beneficial to agricultural soils; we found that it was usually highest in soils that received the organic carbon amendment and lowest in those with soil sterilization. However, tree vigor was highest with the sterilization treatments. The effects of a microbial inoculants/organic carbon combination on microbial communities and plant vigor were no different from simply adding organic carbon.

Widespread contamination of groundwater by MTBE has triggered the exploration of different technologies for in situ removal of the pollutant. After laboratory studies revealed that bacterial strain PMl is capable of rapid and complete MTBE biodegradation, the organism was tested in an in-situ bioaugmentation field study at Port Hueneme Naval Base, Oxnard, CA. Two small pilot test plots (A and B) located down gradient from an MTBE source were injected with pure oxygen at two depths. One plot (B) was also inoculated with Strain PMl. MTBE concentrations upstream from plots A and B initially varied temporally from 1.5 to 6 mg per L. By six months after treatment began, MTBE concentrations wells downstream from the injection bed substantially decreased in the shallow zone of the groundwater in both plots, even in the absence of Strain PM 1. In the deeper zone, downstream MTBE concentrations also decreased substantially in Plot A and to lesser extent in Plot B. Difficulties in delivery of oxygen to the deep zone of Plot B, evidenced by low dissolved oxygen concentrations, are likely responsible for low rates of MTBE removal at that location. We measured the survival and movement of PMl in groundwater using three different methods for detection of PMl rDNA sequences: TaqMan quantitative peR, Denaturing Gradient Gel Electrophoresis (DGGE), and Intergenic Spacer Region (ITS) analysis. A naturally occurring organism with >99% rDNA sequence similarity to Strain PMl was detected in groundwater collected outside the test plots. Changes in the groundwater microbial community were also monitored over time using ITS, a PCR-based DNA fingerprinting method. The largest differences in the microbial community profiles were observed between the shallow and deep groundwater samples, regardless of whether they were from plot A or B.